A steady downpour of rain fell over Oakland and the Bay Area on Friday morning.

Photo: SF Gate / Douglas Zimmerman

A steady downpour of rain fell over Oakland and the Bay Area on...

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A water vapor view of the western United States is seen in a NOAA image taken from the GOES-West satellite at 05:00 PST February 28, 2014. A strong storm system moving into the region will bring heavy rain, gusty wind, possible thunderstorms and waterspouts, and high elevation snow through late Saturday, according to the National Weather Service.

Photo: Noaa, Reuters

A water vapor view of the western United States is seen in a NOAA...

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Bidur Pokharel shields himself from the rain as he bikes along Yulupa Avenue in Santa Rosa, Calif., Wednesday, Feb. 26, 2014. Much-needed rain fell in Northern California on Wednesday at the outset of what the parched state hopes is the start to a one-two punch of stormy weather with a half inch of rain predicted.

Photo: Christopher Chung, Associated Press

Bidur Pokharel shields himself from the rain as he bikes along...

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A woman with a rainbow umbrella waits to cross Market Street during a rain storm in San Francisco, California, February 26, 2014. REUTERS/Beck Diefenbach (UNITED STATES - Tags: ENVIRONMENT SOCIETY)

Photo: Beck Diefenbach, Reuters

A woman with a rainbow umbrella waits to cross Market Street during...

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Volunteers, from left, Steve Hamilton, Thomas Lubboch and Becky Chen help fill sandbags before an expected storm Wednesday Feb. 26, 2014 in Glendora, Calif. Much-needed rain fell in Northern California on Wednesday at the outset of what the parched state hopes is the start to a one-two punch of stormy weather with a half inch of rain predicted. (AP Photo/Nick Ut )

Photo: Nick Ut, Associated Press

Volunteers, from left, Steve Hamilton, Thomas Lubboch and Becky...

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Farmworkers pick broccolini in the rain on Wednesday, Feb. 26, 2014, in King City, Calif. A potentially stronger storm is expected to move in late Thursday, bringing much needed rain in central and southern valleys and snow to the mountains in the drought-stricken state. (AP Photo/Marcio Jose Sanchez)

Photo: Marcio Jose Sanchez, Associated Press

Farmworkers pick broccolini in the rain on Wednesday, Feb. 26,...

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A woman with a flower umbrella crosses the street during a rain storm in San Francisco, California, February 26, 2014. REUTERS/Beck Diefenbach (UNITED STATES - Tags: SOCIETY ENVIRONMENT)

Photo: Beck Diefenbach, Reuters

A woman with a flower umbrella crosses the street during a rain...

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A women walks along Treasure Island with the San Francisco Bay bridge in the background during a rain storm Wednesday, Feb. 26, 2014, in San Francisco. Several winter storms are expected to bring rain to the Bay Area through the end of the week. (AP Photo/Ben Margot)

Photo: Ben Margot, Associated Press

A women walks along Treasure Island with the San Francisco Bay...

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A man walks down Pier 14 during a rain storm in San Francisco, California, February 26, 2014. REUTERS/Beck Diefenbach (UNITED STATES - Tags: ENVIRONMENT SOCIETY)

Photo: Beck Diefenbach, Reuters

A man walks down Pier 14 during a rain storm in San Francisco,...

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A woman's umbrella flips inside out during a rain storm in San Francisco, California, February 26, 2014. REUTERS/Beck Diefenbach (UNITED STATES - Tags: ENVIRONMENT SOCIETY)

The major delays that frustrated BART riders during Friday morning's commute - particularly on trains traveling through the Transbay Tube - were the result of weather-related problems, an agency spokeswoman said.

About 5 a.m., water seeped through a ventilation system at a train control room in San Francisco, which "got some of the computer components wet" and forced BART to hold trains in the area for 12 minutes, said BART spokeswoman Alicia Trost.

Engineers tried repeatedly to reboot the system, and during that time, trains had to be run manually and at a slower speed, causing delays throughout the system of at least half an hour, Trost said.

Some trains had to be turned back to other stations, where passengers were told to get off and then transfer to other trains. It wasn't until 8 a.m. that the system was rebooted.

But an hour later, the heavy rain caused more delays, with "extreme moisture" on the tracks forcing operators of some trains to operate manually, Trost said.